supplementary materials


sj5360 scheme

Acta Cryst. (2013). E69, o1717-o1718    [ doi:10.1107/S1600536813029103 ]

4-Meth­oxy-N-(pyridin-4-ylmeth­yl)-3-(tri­fluoro­meth­yl)benzamide monohydrate

S. Sreenivasa, N. R. Mohan, V. Kumar, B. S. Palakshamurthy, D. B. Arunakumar and P. A. Suchetan

Abstract top

In the title compound, C15H13F3N2O2·H2O, the dihedral angle between the benzene and pyridine rings is 74.97 (1)°. The -CF3 group attached to the benzene ring is syn to the C=O bond in the adjacent side chain. In the crystal, mol­ecules are linked to one another through the water mol­ecules by strong N-H...O, O-H...O and O-H...N hydrogen bonds, forming a ladder-type network. The benzamide mol­ecules are also linked to one another through C-H...F inter­actions, forming C(6) chains parallel to the b-axis direction. Aromatic [pi]-[pi] stacking inter­actions [centroid-centroid separations = 3.7150 (1) and 3.7857 (1) Å] between adjacent pairs of pyridine and benzene rings are also observed, resulting in a three-dimensional architecture are also observed.

Comment top

Amides containing trifluoromethyl substituents have been considered as important pharmacophores (Sreenivasa et al. 2013a). Amide groups are very common in nature, form easily and provide structural rigidity to molecules (Sreenivasa et al. 2013b). Amides show a broad spectrum of pharmacological properties, including antibacterial (Manojkumar et al. 2013a), anti-inflammatory, antioxidant, analgesic and antiviral activity (Manojkumar et al. 2013b, Sreenivasa et al. 2013c). Keeping this in mind, the crystal structure of the title compound was determined.

In the title compound, C15H13F3N2O2·H2O, the dihedral angle between the benzene ring and the pyridine ring is 74.97 (1)°. The –CF3 group attached to the benzene ring is syn to the C=O bond in the adjacent side chain. Further, the conformation of the N—H bond in the chain is anti with respect to the C=O bond. In the crystal structure, the molecules are linked to one another via water molecules through strong N1—HN1···O3, O3—H2O···O2 and O3—H1O···N2 hydrogen bonds, forming a ladder type network. The benzamide molecules are also linked to one another forming C(6) chains (Bernstein et al., 1995) parallel to the b axis through intermolecular C6—H6···F3 interactions. Further, aromatic ππ stacking interactions [centroid-centroid separations Cg1···Cg1 = 3.7150 (1) Å and Cg2···Cg2 = 3.7857 (1) Å] are also observed in the crystal structure. Cg1 and Cg2 are the centroids of the C11···C13,N2,C14,C15 and C1···C6 rings respectively.

Related literature top

For hydrogen-bond motifs, see: Bernstein et al. (1995). For the biological activity of amides, see: Manojkumar et al. (2013a,b); Sreenivasa et al. (2013c). For the importance of amides containing trifluoromethyl substituents as pharmacophores, see: Sreenivasa et al. (2013a) and for amides providing structural rigidity to the molecules, see: Sreenivasa et al. (2013b).

Experimental top

3-Tri-fluoromethyl-4-methoxy benzoic acid (1 mmol) and 1,1-carbonyldiimidazole (1.5 mmol) were dissolved in dichloroethane (5 ml) and heated to 45 oC for 30 min. 4-Aminomethyl pyridine (1.5 mmol) was added and the heating was continued for 4 h. The reaction was monitored by TLC. The organic layer was washed with sodium bicarbonate, dried using sodium sulfate and concentrated to yield the crude compound. This was further purified by column chromatography using petroleum ether / ethyl acetate (7:3) as eluent. Fine colorless crystals were grown by slow evaporation of the solvent system: petroleum ether / ethyl acetate (4:1) at room temperature.

Refinement top

The hydrogen atoms attached to O3 were located in difference maps and refined in a rigid group. The remaining H atoms were positioned with idealized geometry using a riding model with N–H = 0.86 and C—H = 0.93 - 0.97 Å. The isotropic displacement parameters for all H atoms were set to 1.2 times Ueq of the parent atom or 1.5 times that of the parent atom for CH3.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: APEX2 and SAINT-Plus (Bruker, 2009); data reduction: SAINT-Plus and XPREP (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Linking of molecules in the crystal structure via water molecules, generating a ladder type network. H-atoms not involved in H-bonding are omitted.
[Figure 3] Fig. 3. Linking of molecules into C(6) chains parallel to the b axis through C—H···F interactions.
[Figure 4] Fig. 4. Aromatic ππ stacking interactions observed in the crystal structure.
4-Methoxy-N-(pyridin-4-ylmethyl)-3-(trifluoromethyl)benzamide monohydrate top
Crystal data top
C15H13F3N2O2·H2OF(000) = 340
Mr = 328.29Prism
Triclinic, P1Dx = 1.427 Mg m3
Hall symbol: -P 1Melting point: 485 K
a = 7.2687 (13) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.8758 (14) ÅCell parameters from 1167 reflections
c = 14.177 (3) Åθ = 1.5–25.0°
α = 104.071 (10)°µ = 0.12 mm1
β = 99.672 (10)°T = 296 K
γ = 97.21 (1)°Prism, colourless
V = 764.2 (2) Å30.34 × 0.28 × 0.22 mm
Z = 2
Data collection top
Bruker APEXII CCD
diffractometer
11967 independent reflections
Radiation source: fine-focus sealed tube9619 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.000
φ and ω scansθmax = 25.0°, θmin = 1.5°
Absorption correction: ψ scan
(SADABS; Bruker, 2009)
h = 88
Tmin = 0.959, Tmax = 0.973k = 99
11967 measured reflectionsl = 1616
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.135H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0568P)2 + 0.2647P]
where P = (Fo2 + 2Fc2)/3
11967 reflections(Δ/σ)max = 0.001
212 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = 0.34 e Å3
Crystal data top
C15H13F3N2O2·H2Oγ = 97.21 (1)°
Mr = 328.29V = 764.2 (2) Å3
Triclinic, P1Z = 2
a = 7.2687 (13) ÅMo Kα radiation
b = 7.8758 (14) ŵ = 0.12 mm1
c = 14.177 (3) ÅT = 296 K
α = 104.071 (10)°0.34 × 0.28 × 0.22 mm
β = 99.672 (10)°
Data collection top
Bruker APEXII CCD
diffractometer
11967 independent reflections
Absorption correction: ψ scan
(SADABS; Bruker, 2009)
9619 reflections with I > 2σ(I)
Tmin = 0.959, Tmax = 0.973Rint = 0.000
11967 measured reflectionsθmax = 25.0°
Refinement top
R[F2 > 2σ(F2)] = 0.048H-atom parameters constrained
wR(F2) = 0.135Δρmax = 0.36 e Å3
S = 1.06Δρmin = 0.34 e Å3
11967 reflectionsAbsolute structure: ?
212 parametersAbsolute structure parameter: ?
0 restraintsRogers parameter: ?
Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C40.20712 (13)0.16715 (12)0.35758 (7)0.0408 (2)
C10.26262 (13)0.00741 (12)0.56032 (7)0.0417 (3)
C60.24913 (15)0.10202 (13)0.48940 (8)0.0468 (3)
H60.25890.22490.50920.056*
C50.22150 (14)0.01550 (13)0.39008 (8)0.0468 (3)
H50.21230.08120.34370.056*
C70.2577 (2)0.28518 (15)0.60207 (9)0.0678 (4)
C30.22117 (14)0.26116 (13)0.42910 (8)0.0471 (3)
H30.21200.38400.40900.057*
C110.32767 (14)0.24851 (13)0.04242 (7)0.0430 (3)
C120.49099 (15)0.13759 (13)0.09862 (7)0.0471 (3)
H120.49280.07020.16260.057*
C90.18106 (15)0.26938 (14)0.25155 (8)0.0488 (3)
C20.24823 (14)0.17729 (13)0.52871 (8)0.0452 (3)
C100.14376 (16)0.26534 (16)0.07791 (8)0.0605 (3)
H10A0.05390.21480.03900.073*
H10B0.09310.39060.06490.073*
C130.65231 (16)0.12678 (14)0.05948 (8)0.0538 (3)
H130.76070.05020.09880.065*
C80.30246 (17)0.26947 (13)0.69388 (8)0.0567 (3)
H8A0.41110.32760.67660.085*
H8B0.31540.30320.76480.085*
H8C0.19010.30420.66350.085*
C140.50371 (19)0.32623 (15)0.08476 (9)0.0641 (3)
H140.50590.39270.14840.077*
C150.33680 (17)0.34444 (14)0.05187 (8)0.0558 (3)
H150.23010.42120.09290.067*
N10.15688 (12)0.18044 (12)0.18228 (6)0.0520 (2)
HN10.14890.06960.20030.062*
N20.66248 (14)0.21897 (12)0.03090 (7)0.0586 (3)
O10.28861 (11)0.08100 (9)0.65917 (5)0.0556 (2)
O30.89123 (14)0.17560 (10)0.17013 (7)0.0713 (3)
H1O0.84110.18090.12070.107*
H2O0.89340.28020.20390.107*
O20.18367 (14)0.43033 (10)0.22891 (6)0.0790 (3)
F10.12080 (15)0.27319 (12)0.65342 (7)0.1170 (3)
F20.41714 (13)0.23917 (11)0.67010 (6)0.1046 (3)
F30.24329 (18)0.45486 (10)0.55973 (6)0.1459 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C40.0431 (6)0.0365 (6)0.0412 (6)0.0039 (5)0.0103 (5)0.0078 (5)
C10.0483 (6)0.0381 (6)0.0362 (6)0.0054 (5)0.0060 (5)0.0083 (5)
C60.0653 (7)0.0322 (6)0.0415 (7)0.0077 (5)0.0093 (5)0.0091 (5)
C50.0609 (7)0.0417 (6)0.0386 (7)0.0070 (5)0.0096 (5)0.0136 (5)
C70.1090 (11)0.0452 (8)0.0500 (8)0.0187 (7)0.0111 (8)0.0155 (6)
C30.0574 (7)0.0307 (6)0.0511 (7)0.0058 (5)0.0106 (5)0.0082 (5)
C110.0548 (6)0.0382 (6)0.0346 (6)0.0066 (5)0.0068 (5)0.0092 (5)
C120.0563 (7)0.0476 (6)0.0328 (6)0.0076 (5)0.0047 (5)0.0060 (5)
C90.0508 (6)0.0430 (7)0.0475 (7)0.0026 (5)0.0119 (5)0.0045 (6)
C20.0566 (7)0.0360 (6)0.0444 (7)0.0081 (5)0.0089 (5)0.0142 (5)
C100.0565 (7)0.0739 (8)0.0378 (7)0.0006 (6)0.0064 (5)0.0013 (6)
C130.0532 (7)0.0541 (7)0.0490 (7)0.0039 (5)0.0024 (6)0.0124 (6)
C80.0814 (8)0.0411 (6)0.0421 (7)0.0100 (6)0.0077 (6)0.0048 (5)
C140.0830 (9)0.0553 (8)0.0476 (7)0.0037 (7)0.0236 (7)0.0009 (6)
C150.0655 (8)0.0478 (7)0.0425 (7)0.0041 (6)0.0120 (6)0.0029 (5)
N10.0636 (6)0.0506 (5)0.0366 (5)0.0064 (4)0.0126 (4)0.0026 (4)
N20.0638 (6)0.0549 (6)0.0572 (7)0.0086 (5)0.0185 (5)0.0120 (5)
O10.0865 (6)0.0409 (4)0.0364 (4)0.0108 (4)0.0067 (4)0.0091 (3)
O30.0933 (6)0.0590 (5)0.0690 (6)0.0117 (5)0.0364 (5)0.0185 (4)
O20.1277 (8)0.0419 (5)0.0609 (6)0.0138 (5)0.0235 (5)0.0004 (4)
F10.1480 (8)0.1277 (8)0.1152 (7)0.0268 (6)0.0619 (7)0.0820 (6)
F20.1252 (7)0.1093 (7)0.0871 (6)0.0239 (5)0.0084 (5)0.0600 (5)
F30.3145 (16)0.0451 (5)0.0806 (6)0.0383 (6)0.0229 (7)0.0305 (4)
Geometric parameters (Å, º) top
C4—C51.3843 (13)C12—H120.9300
C4—C31.3914 (13)C9—O21.2331 (12)
C4—C91.4903 (14)C9—N11.3392 (13)
C1—O11.3506 (12)C10—N11.4495 (13)
C1—C61.3875 (14)C10—H10A0.9700
C1—C21.3989 (13)C10—H10B0.9700
C6—C51.3753 (14)C13—N21.3295 (14)
C6—H60.9300C13—H130.9300
C5—H50.9300C8—O11.4305 (12)
C7—F31.3079 (13)C8—H8A0.9600
C7—F21.3240 (15)C8—H8B0.9600
C7—F11.3279 (16)C8—H8C0.9600
C7—C21.4929 (15)C14—N21.3319 (15)
C3—C21.3746 (14)C14—C151.3743 (16)
C3—H30.9300C14—H140.9300
C11—C121.3750 (14)C15—H150.9300
C11—C151.3832 (14)N1—HN10.8600
C11—C101.5072 (15)O3—H1O0.8499
C12—C131.3808 (15)O3—H2O0.8500
C5—C4—C3117.63 (9)C3—C2—C1119.91 (9)
C5—C4—C9124.51 (9)C3—C2—C7119.49 (9)
C3—C4—C9117.85 (9)C1—C2—C7120.59 (10)
O1—C1—C6124.57 (9)N1—C10—C11115.26 (9)
O1—C1—C2116.78 (8)N1—C10—H10A108.5
C6—C1—C2118.65 (9)C11—C10—H10A108.5
C5—C6—C1120.53 (9)N1—C10—H10B108.5
C5—C6—H6119.7C11—C10—H10B108.5
C1—C6—H6119.7H10A—C10—H10B107.5
C6—C5—C4121.53 (9)N2—C13—C12124.12 (10)
C6—C5—H5119.2N2—C13—H13117.9
C4—C5—H5119.2C12—C13—H13117.9
F3—C7—F2106.29 (11)O1—C8—H8A109.5
F3—C7—F1105.41 (12)O1—C8—H8B109.5
F2—C7—F1104.90 (11)H8A—C8—H8B109.5
F3—C7—C2112.39 (10)O1—C8—H8C109.5
F2—C7—C2113.54 (11)H8A—C8—H8C109.5
F1—C7—C2113.58 (10)H8B—C8—H8C109.5
C2—C3—C4121.74 (9)N2—C14—C15123.86 (11)
C2—C3—H3119.1N2—C14—H14118.1
C4—C3—H3119.1C15—C14—H14118.1
C12—C11—C15116.65 (10)C14—C15—C11119.91 (11)
C12—C11—C10123.31 (10)C14—C15—H15120.0
C15—C11—C10120.02 (9)C11—C15—H15120.0
C11—C12—C13119.61 (10)C9—N1—C10121.98 (10)
C11—C12—H12120.2C9—N1—HN1119.0
C13—C12—H12120.2C10—N1—HN1119.0
O2—C9—N1121.38 (10)C13—N2—C14115.85 (10)
O2—C9—C4120.76 (10)C1—O1—C8118.17 (7)
N1—C9—C4117.85 (9)H1O—O3—H2O109.5
O1—C1—C6—C5179.63 (9)F3—C7—C2—C31.81 (18)
C2—C1—C6—C50.23 (15)F2—C7—C2—C3122.49 (12)
C1—C6—C5—C40.29 (16)F1—C7—C2—C3117.75 (12)
C3—C4—C5—C60.15 (15)F3—C7—C2—C1179.53 (12)
C9—C4—C5—C6178.73 (10)F2—C7—C2—C158.85 (15)
C5—C4—C3—C20.05 (15)F1—C7—C2—C160.90 (15)
C9—C4—C3—C2179.00 (9)C12—C11—C10—N110.41 (15)
C15—C11—C12—C130.16 (14)C15—C11—C10—N1171.11 (10)
C10—C11—C12—C13178.37 (9)C11—C12—C13—N20.43 (16)
C5—C4—C9—O2174.51 (10)N2—C14—C15—C110.26 (18)
C3—C4—C9—O24.36 (15)C12—C11—C15—C140.16 (15)
C5—C4—C9—N14.80 (15)C10—C11—C15—C14178.74 (10)
C3—C4—C9—N1176.33 (9)O2—C9—N1—C103.73 (16)
C4—C3—C2—C10.10 (16)C4—C9—N1—C10175.58 (9)
C4—C3—C2—C7178.57 (10)C11—C10—N1—C993.86 (12)
O1—C1—C2—C3179.83 (9)C12—C13—N2—C140.33 (16)
C6—C1—C2—C30.04 (15)C15—C14—N2—C130.02 (17)
O1—C1—C2—C71.17 (15)C6—C1—O1—C80.32 (15)
C6—C1—C2—C7178.69 (10)C2—C1—O1—C8179.53 (9)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—HN1···O3i0.862.122.9119 (14)152
O3—H1O···N20.852.012.8402 (15)166
O3—H2O···O2ii0.852.202.9646 (13)149
C6—H6···F3iii0.932.463.3963 (15)173
Symmetry codes: (i) x+1, y, z; (ii) x+1, y1, z; (iii) x, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—HN1···O3i0.862.122.9119 (14)152
O3—H1O···N20.852.012.8402 (15)166
O3—H2O···O2ii0.852.202.9646 (13)149
C6—H6···F3iii0.932.463.3963 (15)173
Symmetry codes: (i) x+1, y, z; (ii) x+1, y1, z; (iii) x, y+1, z.
Acknowledgements top

The authors thank Professor T. N. Guru Row, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, for his help and valuable suggestions.

references
References top

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Manojkumar, K. E., Sreenivasa, S., Shivaraja, G. & Madhuchakrapani Rao, T. (2013b). Molbank. M803; doi:10.3390/M803.

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Sreenivasa, S., ManojKumar, K. E., Suchetan, P. A., Tonannavar, J., Chavan, Y. & Palakshamurthy, B. S. (2013b). Acta Cryst. E69, o185.

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